LAMMPS (28 Mar 2023 - Development)
  using 1 OpenMP thread(s) per MPI task
# 2d rounded polygon bodies

variable    r     index 4
variable    steps index 100000
variable    T     index 0.5
variable    P     index 0.1
variable    seed  index 980411

units       lj
dimension   2

atom_style  body rounded/polygon 1 6
atom_modify map array
read_data   data.squares
Reading data file ...
  orthogonal box = (0 0 -0.5) to (12 12 0.5)
  2 by 2 by 1 MPI processor grid
  reading atoms ...
  2 atoms
  2 bodies
  read_data CPU = 0.001 seconds

replicate   $r $r 1
replicate   4 $r 1
replicate   4 4 1
Replication is creating a 4x4x1 = 16 times larger system...
  orthogonal box = (0 0 -0.5) to (48 48 0.5)
  2 by 2 by 1 MPI processor grid
  32 atoms
  replicate CPU = 0.001 seconds

velocity    all create $T ${seed} dist gaussian mom yes rot yes
velocity    all create 0.5 ${seed} dist gaussian mom yes rot yes
velocity    all create 0.5 980411 dist gaussian mom yes rot yes

change_box  all boundary p f p
Changing box ...

variable cut_inner  equal 0.5
variable k_n        equal 100
variable k_na       equal 2
variable c_n        equal 0.1
variable c_t        equal 0.1
variable mu         equal 0.1
variable delta_ua   equal 0.5

pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 0.1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 0.1 0.1 ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 0.1 0.1 0.1 ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 ${cut_inner}
pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 0.5
pair_coeff * * ${k_n} ${k_na}
pair_coeff * * 100 ${k_na}
pair_coeff * * 100 2

comm_modify vel yes

neighbor     0.5 bin
neigh_modify every 1 delay 0 check yes

timestep     0.001

#fix         1 all nve/body
#fix         1 all nvt/body temp $T $T 1.0
fix          1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
fix          1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 fixedpoint 0 0 0

fix          2 all enforce2d
fix          3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0

#compute      1 all body/local id 1 2 3
#dump         1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]

thermo_style custom step ke pe etotal press
thermo       1000

#dump	     2 all image 10000 image.*.jpg type type zoom 2.0 #             adiam 1.5 body type 0 0
#dump_modify  2 pad 6

run          ${steps}
run          100000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 6.1568542
  ghost atom cutoff = 6.1568542
  binsize = 3.0784271, bins = 16 16 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair body/rounded/polygon, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/2d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.378 | 5.378 | 5.379 Mbytes
   Step         KinEng         PotEng         TotEng         Press     
         0   0.484375       0.25           0.734375       0.0067274306 
      1000   0.51464289     0.00099012638  0.51563301     0.013444625  
      2000   0.55653313     0.0040982283   0.56063136     0.0034505512 
      3000   0.75323998     0.023578898    0.77681887     0.0036652891 
      4000   0.70044978     0.092406287    0.79285607     0.0089262842 
      5000   0.54548803     0.096501313    0.64198934     0.0051379522 
      6000   0.48208828     0.097798868    0.57988715     0.01529805   
      7000   0.68219182     0.038843949    0.72103577     0.016842202  
      8000   0.53792445     0.01298383     0.55090828     0.0066797984 
      9000   0.49980358     0.029397965    0.52920155     0.0046731992 
     10000   0.48705755     0.10138831     0.58844586    -1.9690665e-05
     11000   0.52151879     0.065897951    0.58741674     0.0049324908 
     12000   0.59065198     0.03929683     0.62994881     0.0014198454 
     13000   0.46076897     0.073363984    0.53413295     0.0057849056 
     14000   0.38058168     0.16336914     0.54395082     0.0099910111 
     15000   0.58924494     0.13219579     0.72144074     0.012781632  
     16000   0.65163924     0.10979538     0.76143462     0.015088945  
     17000   0.51431594     0.036344433    0.55066037     0.001446035  
     18000   0.42677394     0.093297234    0.52007117     0.00093775852
     19000   0.62399853     0.13309136     0.75708989     0.0095351169 
     20000   0.52835966     0.085936455    0.61429611     0.013158115  
     21000   0.42999051     0.12857394     0.55856445     0.024369485  
     22000   0.56770038     0.19738636     0.76508675     0.024211788  
     23000   0.55137392     0.18212359     0.7334975      0.024095463  
     24000   0.6225794      0.13091248     0.75349189     0.032707954  
     25000   0.47106345     0.10241626     0.57347971     0.0059731265 
     26000   0.60567231     0.055894222    0.66156653     0.010614697  
     27000   0.49075416     0.13914345     0.62989761     0.00048442735
     28000   0.48902573     0.21423204     0.70325777     0.021295043  
     29000   0.42728391     0.24136135     0.66864527     0.031633766  
     30000   0.64658635     0.15368867     0.80027502     0.0084616839 
     31000   0.71370199     0.18014549     0.89384748     0.02367184   
     32000   0.40141173     0.1833294      0.58474113     0.034918949  
     33000   0.55780706     0.14130843     0.69911549     0.012266172  
     34000   0.36544303     0.15788143     0.52332446     0.0084938225 
     35000   0.56844142     0.17507842     0.74351984     0.061506713  
     36000   0.5048707      0.15834563     0.66321633     0.0286909    
     37000   0.4371274      0.087735559    0.52486296    -0.0016289252 
     38000   0.49941117     0.22576207     0.72517324     0.059233327  
     39000   0.69480051     0.15465372     0.84945423     0.039061293  
     40000   0.52881719     0.29110071     0.8199179      0.032439208  
     41000   0.56931201     0.38596881     0.95528082     0.045284803  
     42000   0.46759969     0.21337568     0.68097537     0.086759715  
     43000   0.63416318     0.44687151     1.0810347      0.072272415  
     44000   0.43914666     0.20832735     0.64747401     0.026280272  
     45000   0.38329718     0.25407815     0.63737533     0.017356403  
     46000   0.59511045     0.32148788     0.91659833    -0.0076184601 
     47000   0.50635988     0.37243112     0.878791       0.025435347  
     48000   0.42316224     0.29368731     0.71684954     0.00067040329
     49000   0.40194259     0.26659105     0.66853364     0.069225504  
     50000   0.4740342      0.305674       0.77970819     0.014813566  
     51000   0.57279011     0.32080139     0.8935915      0.0091332017 
     52000   0.54543481     0.34482955     0.89026435    -0.021131696  
     53000   0.39241519     0.36432403     0.75673922     0.0077163816 
     54000   0.62021406     0.32010094     0.940315       0.044477965  
     55000   0.45160485     0.29442122     0.74602607     0.02563201   
     56000   0.41737028     0.31207675     0.72944704     0.050342936  
     57000   0.53454189     0.29192181     0.8264637      0.068452573  
     58000   0.65449932     0.33567481     0.99017413     0.055352019  
     59000   0.58742699     0.37317432     0.96060131     0.012805462  
     60000   0.42430458     0.33744246     0.76174704     0.018744436  
     61000   0.65433333     0.40723506     1.0615684      0.019757611  
     62000   0.64472397     0.34658649     0.99131047     0.090688735  
     63000   0.65381774     0.47452792     1.1283457      0.2090513    
     64000   0.44107995     0.60507044     1.0461504      0.03144844   
     65000   0.38159186     0.45527276     0.83686462     0.090856608  
     66000   0.48842595     0.49445721     0.98288316     0.08753844   
     67000   0.65088575     0.4611542      1.11204        0.066602605  
     68000   0.5155131      0.38693864     0.90245174     0.0062596909 
     69000   0.41477899     0.45120406     0.86598306     0.037396561  
     70000   0.60305022     0.47624271     1.0792929      0.040607751  
     71000   0.67077877     0.51044906     1.1812278      0.029084971  
     72000   0.50912034     0.34340114     0.85252148     0.055767674  
     73000   0.55167778     0.43795801     0.98963579     0.083371911  
     74000   0.53603549     0.37357862     0.90961411     0.058762722  
     75000   0.47521522     0.529749       1.0049642      0.12419171   
     76000   0.48952134     0.63953611     1.1290574      0.09709472   
     77000   0.63445283     0.57542295     1.2098758      0.11868116   
     78000   0.62184463     0.60025138     1.222096       0.079417229  
     79000   0.52715665     0.54847579     1.0756324      0.033981154  
     80000   0.6264593      0.39323366     1.019693       0.05627332   
     81000   0.78582235     0.47541992     1.2612423      0.031287815  
     82000   0.69665491     0.58355423     1.2802091     -0.04433392   
     83000   0.4994351      0.40089694     0.90033204    -0.0019687817 
     84000   0.50932093     0.62716285     1.1364838      0.095177695  
     85000   0.56251638     0.56010929     1.1226257      0.013989132  
     86000   0.67155822     0.51326814     1.1848264      0.10616402   
     87000   0.61317511     0.52704394     1.140219       0.076578899  
     88000   0.57436568     0.60641096     1.1807766      0.042050421  
     89000   0.62350614     0.65896923     1.2824754      0.15949038   
     90000   0.57445242     0.65085438     1.2253068      0.034123951  
     91000   0.50043488     0.69213026     1.1925651     -0.076403957  
     92000   0.57345231     0.74801993     1.3214722      0.033715387  
     93000   0.63056204     0.64474627     1.2753083      0.051205732  
     94000   0.70948937     0.61081243     1.3203018     -0.0069457836 
     95000   0.66048722     0.61001641     1.2705036      0.16072266   
     96000   0.48720026     0.64888522     1.1360855      0.12573765   
     97000   0.41570988     0.68810987     1.1038198     -0.033070846  
     98000   0.53689925     0.83787736     1.3747766      0.098173219  
     99000   0.5147061      0.92360546     1.4383116      0.12155736   
    100000   0.5793939      0.63393822     1.2133321      0.090967465  
Loop time of 2.08698 on 4 procs for 100000 steps with 32 atoms

Performance: 4139957.491 tau/day, 47916.175 timesteps/s, 1.533 Matom-step/s
92.1% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.31       | 0.33594    | 0.35254    |   2.8 | 16.10
Neigh   | 0.001991   | 0.0021241  | 0.0022581  |   0.2 |  0.10
Comm    | 0.40717    | 0.43106    | 0.46731    |   3.4 | 20.65
Output  | 0.00076842 | 0.002908   | 0.0092082  |   6.7 |  0.14
Modify  | 1.1389     | 1.1624     | 1.1753     |   1.3 | 55.70
Other   |            | 0.1525     |            |       |  7.31

Nlocal:              8 ave           9 max           7 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost:             14 ave          16 max          12 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs:          13.25 ave          17 max          11 min
Histogram: 1 1 0 1 0 0 0 0 0 1

Total # of neighbors = 53
Ave neighs/atom = 1.65625
Neighbor list builds = 3000
Dangerous builds = 0
Total wall time: 0:00:02
